If you check your files (using ls -l) you should see that the Makefile is newly created. The prefix that you specified is taken in by configure and put into Makefile. So when do you make and make install, the make will take the prefix and put the files into where you specified as prefix.

./configure (This creates the makefile setting paths to various commands, works out architecture and optimisations and any other bits requires)
make (Normally this compiles the code)
make install (Normally this bit does the installing)

Various customisations relating to directories etc are often possible. The correct place to specify these, and the various 'make' options e.g.:

make
make install
make clean (Conventionally used to delete all *.o files before recompiling)
make uninstall (Not always avaialble)

are conventionally detailed in either the README.txt oe INSTALL.txt file or similar. Obviously depending on the programmer, he could change the various options to whatever they think would be of use for the program.

1) Download maildrop
2) Unpack it (tar xjf courier-sox-0.06.tar.bz2)
3) cd courier-sox-0.06
3.1) At this moment, you can check and you will find that there is no Makefile (there is Makefile.am and Makefile.in, but not Makefile).
4) If you only do ./configure, maildrop will be installed into /usr/local by default. If you want to install it into /usr instead of /usr/local, you should do ./configure --prefix=/usr
5) Next you do "make" to compile the programs (after make the programs are not installed yet).
6) After that you do "make install" then the programs will be installed into (if you --prefix=/usr) /usr/lib two file: "libsocks.so" and "libsockswrap.so", /usr/bin/socksify, /usr/include/socks.h, and some other files... (You can read up in the INSTALL file).

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